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Literature DB >> 12638011

Binding site characteristics in structure-based virtual screening: evaluation of current docking tools.

Abstract

Two new docking programs FRED (OpenEye Scientific Software) and Glide (Schrödinger, Inc.) in combination with various scoring functions implemented in these programs have been evaluated against a variety of seven protein targets (cyclooxygenase-2, estrogen receptor, p38 MAP kinase, gyrase B, thrombin, gelatinase A, neuraminidase) in order to assess their accuracy in virtual screening. Sets of known inhibitors were added to and ranked relative to a random library of drug-like compounds. Performance was compared in terms of enrichment factors and CPU time consumption. Results and specific features of the two new tools are discussed and compared to previously published results using FlexX (Tripos, Inc.) as a docking engine. In addition, general criteria for the selection of docking algorithms and scoring functions based on binding-site characteristics of specific protein targets are proposed. Figure Enrichment factors obtained with FlexX, Glide and FRED docking engines in combination with different scoring functions for seven selected targets with highly variable binding sites

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Year: 2003 PMID： 12638011 DOI： 10.1007/s00894-002-0112-y

Source DB: PubMed Journal: J Mol Model ISSN： 0948-5023 Impact factor: 1.810

26 in total

Review 1. Statistical potentials and scoring functions applied to protein-ligand binding.

Authors: H Gohlke; G Klebe
Journal: Curr Opin Struct Biol Date: 2001-04 Impact factor: 6.809

2. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

Authors: P S Charifson; J J Corkery; M A Murcko; W P Walters
Journal: J Med Chem Date: 1999-12-16 Impact factor: 7.446

3. Scoring functions: a view from the bench.

Authors: J R Tame
Journal: J Comput Aided Mol Des Date: 1999-03 Impact factor: 3.686

4. High-throughput chemistry and structure-based design: survival of the smartest.

Authors: D Bailey; D Brown
Journal: Drug Discov Today Date: 2001-01-01 Impact factor: 7.851

Review 5. Recent advances in structure-based rational drug design.

Authors: P J Gane; P M Dean
Journal: Curr Opin Struct Biol Date: 2000-08 Impact factor: 6.809

6. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

Authors: M D Eldridge; C W Murray; T R Auton; G V Paolini; R P Mee
Journal: J Comput Aided Mol Des Date: 1997-09 Impact factor: 3.686

7. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4.

Authors: G M Morris; D S Goodsell; R Huey; A J Olson
Journal: J Comput Aided Mol Des Date: 1996-08 Impact factor: 3.686

8. Development and validation of a genetic algorithm for flexible docking.

Authors: G Jones; P Willett; R C Glen; A R Leach; R Taylor
Journal: J Mol Biol Date: 1997-04-04 Impact factor: 5.469

9. Structure-based design of inhibitors of the rice blast fungal enzyme trihydroxynaphthalene reductase.

Authors: D B Jordan; G S Basarab; D I Liao; W M Johnson; K N Winzenberg; D A Winkler
Journal: J Mol Graph Model Date: 2001 Impact factor: 2.518

Review 10. Thrombin inhibitor design.

Authors: P E Sanderson; A M Naylor-Olsen
Journal: Curr Med Chem Date: 1998-08 Impact factor: 4.530

36 in total

Binding site characteristics in structure-based virtual screening: evaluation of current docking tools.

Review 1. Statistical potentials and scoring functions applied to protein-ligand binding.

2. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

3. Scoring functions: a view from the bench.

4. High-throughput chemistry and structure-based design: survival of the smartest.

Review 5. Recent advances in structure-based rational drug design.

6. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

7. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4.

8. Development and validation of a genetic algorithm for flexible docking.

9. Structure-based design of inhibitors of the rice blast fungal enzyme trihydroxynaphthalene reductase.

Review 10. Thrombin inhibitor design.

1. Making virtual screening a reality.

2. Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock.

3. Improving molecular docking through eHiTS' tunable scoring function.

4. Biased retrieval of chemical series in receptor-based virtual screening.

5. ProPose: a docking engine based on a fully configurable protein-ligand interaction model.

6. Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase.

7. A fast surface-matching procedure for protein-ligand docking.

8. Benchmarking sets for molecular docking.

Review 9. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

10. Homology Modeling and Protein Interaction Map of CHRNA7 Neurogenesis Protein.